Hi Wei,
your double bond is clearly not correctly defined in your cif file.
It should be significantly shorter - 1.3A instead of 1.5A.
However, it is easy to edit the expected values manually into your cif file.
Try to find PAM.cif in your coot directory (palmitoleate) to find the
correct value.
Be careful that you edit the correct bond. Your numbering might be
different.
Are you sure that there is no cif file for your ligand already existing?
Best, Matthias
-----------------------------------------
Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK
Phone (+44) 1865 287549;
Fax (+44) 1865 287547
Email matth...@strubi.ox.ac.uk
Website http://www.strubi.ox.ac.uk
-----------------------------------------
On 8/20/2014 3:45 PM, Wei Shi wrote:
Hi all,
I am working on solving a X-ray crystallographic protein-ligand
structures.
Attached please find initial oleoyl-CoA structure (elbow.001.pdb) and
the ligand structure in the final model (ligand in structure.pdb).
When open these in pymol and use "show as lines and set valence, 0.1"
to show double bond, the double bond between C9 and C10 in oleoyl-CoA
fatty acid part is only visible in the initial ligand structure
(elbow.001.pdb) but not in the ligand in the final model (ligand in
structure.pdb). I got the initial ligand using smile string by Phenix.
eLBOW and fit the initial ligand to the electron density, and then
refine the structure in the presence of cif file.
I am wondering whether any of you happen to know why in the final
model (ligand in structure.pdb), double bond (C9) is not visible. Is
it because the double bond is missing or is it because I didn't
display it correctly? Thank you so much!
Best,
Wei
